HIV-1 drug resistance: Where do polymorphisms fit in?

Future Microbiology

Volumn 8, Issue 3, 2013, Pages 303-306

  Theys, Kristof ^a   Abecasis, Ana B ^b   Vandamme, Anne Mieke ^a,b  

^a REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^b UNIVERSIDADE NOVA DE LISBOA   (Portugal)

Author keywords

adaptation; diversity; evolution; fitness; therapy; virulence; virus

Indexed keywords

ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; PROTEINASE INHIBITOR;

ANTIVIRAL RESISTANCE; ANTIVIRAL SUSCEPTIBILITY; GENE MUTATION; GENE SEQUENCE; GENETIC EPISTASIS; GENOTYPE; HUMAN IMMUNODEFICIENCY VIRUS 1; IN VITRO STUDY; NONHUMAN; PHENOTYPE; PLASTICITY; PREDICTION; PRIORITY JOURNAL; REVIEW; VIRUS REPLICATION; VIRUS RESISTANCE;

ANTI-HIV AGENTS; DRUG RESISTANCE, VIRAL; EVOLUTION, MOLECULAR; HIV INFECTIONS; HIV-1; HUMANS; POLYMORPHISM, GENETIC; RNA, VIRAL; VIRULENCE;

EID: 84874736183     PISSN: 17460913     EISSN: 17460921     Source Type: Journal    
DOI: 10.2217/fmb.13.10     Document Type: Review

References (19)

1. Kozal MJ, Shah N, Shen Net al. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat. Med. 2(7), 753-759 (1996).
2. Rhee SY, Taylor J, Fessel WJ et al. HIV-1 protease mutations and protease inhibitor cross-resistance. Antimicrob. Agents Chemother. 54(10), 4253-4261 (2010).
3. Ceccherini-Silberstein F, Erba F, Gago F et al. Identification of the minimal conserved structure of HIV-1 protease in the presence and absence of drug pressure. AIDS 18(12), F11-F9 (2004).
4. Abecasis AB, Deforche K, Bacheler LT et al. Investigation of baseline susceptibility to protease inhibitors in HIV-1 subtypes C, F, G and CRF02-AG. Antivir. Ther. 11(5), 581-589 (2006).
5. Santos AF, Soares MA. HIV genetic diversity and drug resistance. Viruses. 2(2), 503-531 (2010).
6. Rhee SY, Gonzales MJ, Kantor R, Betts BJ, Ravela J, Shafer RW. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res. 31(1), 298-303 (2003).
7. Deforche K, Camacho R, Van Laethem K et al. Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment. Bioinformatics 24(1), 34-41 (2008).
8. Theys K, Deforche K, Beheydt G et al. Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape. BMC Bioinform. 11, 409 (2010).
9. Deforche K, Cozzi-Lepri A, Theys K et al. Modelled in vivo HIV fitness under drug selective pressure and estimated genetic barrier towards resistance are predictive for virological response. Antivir. Ther. 13(3), 399-407 (2008).
10. Martinez-Picado J, Martínez MA. HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo. Virus Res. 134(1-2), 104-123 (2008).
11. Theys K, Deforche K, Vercauteren J et al. Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients. Retrovirology 9, 81 (2012).
12. Arts EJ. Commentary on the role of treatment-related HIV compensatory mutations on increasing virulence: new discoveries twenty years since the clinical testing of protease inhibitors to block HIV-1 replication. BMC Med. 10, 114 (2012).
13. Skowron G, Spritzler JG, Weidler J et al. Replication capacity in relation to immunologic and virologic outcomes in HIV-1-infected treatment-naive subjects. J. Acquir. Immune Defic. Syndr. 50(3), 250-258 (2009).
14. Carlson JM, Brumme ZL. HIV evolution in response to HLA-restricted CTL selection pressures: a population-based perspective. Microbes Infect. 10(5), 455-461 (2008).
15. Matthews PC, Leslie AJ, Katzourakis A et al. HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering. J. Virol. 83(9), 4605-4615 (2009).
16. Leslie A, Kavanagh D, Honeyborne I et al. Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J. Exp. Med. 201(6), 891-902 (2005).
17. Kawashima Y, Pfafferott K, Frater J et al. Adaptation of HIV-1 to human leukocyte antigen class I. Nature 458(7238), 641-645 (2009).
18. Fraser C, Hollingsworth TD, Chapman R, de Wolf F, Hanage WP. Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis. Proc. Natl Acad. Sci. USA 104(44), 17441-17446 (2007).
19. Shirreff G, Pellis L, Laeyendecker O, Fraser C. Transmission selects for HIV-1 strains of intermediate virulence: a modelling approach. PLoS Comput. Biol. 7(10), e1002185 (2011).